Dynam的ic-Programming Strategies for Analyzing Biomolecular Sequences.pptVIP

Kun-Mao Chao Dynamic-Programming Strategies for Analyzing Biomolecular Sequences Kun-Mao Chao Department of Life Science National Yang-Ming University, Taiwan 2002 in Singapore E-mail: kmchao@.tw WWW: .tw/~kmchao Dynamic Programming Dynamic programming is a class of solution methods for solving sequential decision problems with a compositional cost structure. Richard Bellman was one of the principal founders of this approach. Two key ingredients Two key ingredients for an optimization problem to be suitable for a dynamic-programming solution: Three basic components The development of a dynamic-programming algorithm has three basic components: The recurrence relation (for defining the value of an optimal solution); The tabular computation (for computing the value of an optimal solution); The traceback (for delivering an optimal solution). Fibonacci numbers How to compute F10？ Tabular computation The tabular computation can avoid recompuation. Maximum-sum interval Given a sequence of real numbers a1a2…an , find a consecutive subsequence with the maximum sum. O-notation: an asymptotic upper bound f(n) = O(g(n)) iff there exist two positive constant c and n0 such that 0 f(n) cg(n) for all n n0 How functions grow? For large data sets, algorithms with a complexity greater than O(n log n) are often impractical! Maximum-sum interval(The recurrence relation) Define S(i) to be the maximum sum of the intervals ending at position i. Maximum-sum interval(Tabular computation) Maximum-sum interval(Traceback) Defining scores for alignment columns infocon [Stojanovic et al., 1999] Each column is assigned a score that measures its information content, based on the frequencies of the letters both within the column and within the alignment. Defining scores (cont’d) phylogen [Stojanovic et al., 1999] columns are scored based on the evolutionary relationships among the sequences implied by a supplied phylogenetic tree. Two fundamental problems we recently solved (